Merging PDFs sounds like it should be lossless by default, you're just combining files that already exist, not creating new content. In practice, quality and structure loss happens for two separate reasons: some merge tools re-encode images to normalize the combined file, and most tools don't automatically carry over each source document's internal bookmark structure (its navigation outline) unless they're specifically built to.
Why quality loss happens during a merge
A well-built merge tool copies each page's underlying content streams, images, and fonts directly rather than converting pages to a flattened image and rebuilding them, which is why merging is normally lossless for both text sharpness and image resolution. Quality loss creeps in when a tool applies compression as part of the merge process, often silently, to keep the combined file size manageable. If a merged file looks noticeably softer than its originals, it's worth checking whether the tool has a quality or compression setting and setting it to maximum before merging.
The Merge PDF tool preserves each source file's original image and text data during combination, so running your files through it shouldn't introduce visible degradation, but it's still good practice to review a few pages from each source file after merging, particularly image-heavy ones, before sending the combined document anywhere important.
What happens to bookmarks
Bookmarks (also called the outline or table of contents in a PDF's internal structure) are a separate layer of data from the visible pages, essentially a list of named jumps to specific pages. When files are merged, each source document's bookmarks need to be re-mapped to the new page numbers in the combined file, since page 1 of the second document might now be page 45 overall. Tools that don't handle this simply drop the bookmarks rather than risk broken links.
If a combined document needs working navigation, it's worth adding fresh bookmarks after merging rather than assuming the originals carried over, using Organize PDF to reorder pages and rebuild a clean outline once everything is in its final sequence.
Getting page order right before merging
The most common merge mistake isn't quality loss, it's page order: files get combined in alphabetical filename order rather than logical reading order. Renaming files with numeric prefixes (01-cover.pdf, 02-body.pdf) before merging avoids this, or merging first and then using Organize PDF to drag pages into the correct sequence and delete any duplicates that snuck in from overlapping cover pages.